Due to how close the motherboard mounts to the grills its impossible to get a 120x120x25 fan to fit(inside the case). Thermaltake couldn't have built this case with two places for fans that are not usable could they?
I do not have the V3 But on the spec page they state that the top is for 120x120x25mm fan, and by the pics you should be clear of the motherboard when you install the fan, it's not a problem if the fan covers a part of it as long as you don't have to bend things to make it fit. And the right side fan would by the loks of things sit little above your ram. I found this that may be of some use to you.
I do have this case and am running into the same problem. However it is no a matter of just covering something on the Motherboard. The issue is that in order to hit the mounting holes, you need to unlock the Ram clips ( i do not advise this lol). I wanted a top exhaust fan for this case, and purchased 2 Thermaltake Thunderblades to help with this. Needless to say, i ended up bottom mounting for additional intake. I will look at the Yate Loon fans to see if this will work for me.